Mercurial > repos > tduigou > rptools_rpthermo

comparison test-data/scored_pathway.xml @ 0:e9d05fc83186 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
author tduigou
date Tue, 28 Mar 2023 12:08:14 +0000
parents
children d08a18c6167c
comparison
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-1:000000000000 0:e9d05fc83186
1 <?xml version="1.0" encoding="UTF-8"?>
2 <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" level="3" version="1" groups:required="false" fbc:required="false">
3 <model metaid="df484cacc87fa9b4c456e5cff8b987518115bb998c2f7ce8d76e46ebc4ce7a50" id="rp_001_0001" name="rp_001_0001" substanceUnits="mole" timeUnits="second" extentUnits="mole" fbc:strict="true">
4 <listOfCompartments>
5 <compartment metaid="_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6" sboTerm="SBO:0000290" id="c" name="cytosol" size="1" constant="true">
6 <annotation>
7 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
8 <rdf:Description rdf:about="#_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6">
9 <bqbiol:is>
10 <rdf:Bag>
11 <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c"/>
12 <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c_c"/>
13 <rdf:li rdf:resource="http://identifiers.org/metanetx.compartment/MNXC3"/>
14 <rdf:li rdf:resource="http://identifiers.org/seed/c"/>
15 <rdf:li rdf:resource="http://identifiers.org/seed/c0"/>
16 <rdf:li rdf:resource="http://identifiers.org/seed/cytosol"/>
17 <rdf:li rdf:resource="http://identifiers.org/name/cytosol"/>
18 </rdf:Bag>
19 </bqbiol:is>
20 </rdf:Description>
21 </rdf:RDF>
22 </annotation>
23 </compartment>
24 </listOfCompartments>
25 <listOfSpecies>
26 <species metaid="fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9" id="MNXM97" name="MNXM97" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
27 <annotation>
28 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
29 <rdf:Description rdf:about="#fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9">
30 <bqbiol:is>
31 <rdf:Bag/>
32 </bqbiol:is>
33 </rdf:Description>
34 <rdf:BRSynth rdf:about="#fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9">
35 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
36 <brsynth:smiles value="[H]OC(=O)C([H])(N([H])[H])C([H])([H])c1c([H])c([H])c([H])c([H])c1[H]"/>
37 <brsynth:inchi value="InChI=1S/C9H11NO2/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-5,8H,6,10H2,(H,11,12)"/>
38 <brsynth:inchikey value="COLNVLDHVKWLRT-UHFFFAOYSA-N"/>
39 </brsynth:brsynth>
40 </rdf:BRSynth>
41 </rdf:RDF>
42 </annotation>
43 </species>
44 <species metaid="_7d22781170c09f66099e3d92f82fe456ce2c3f02d9162656e7ca49a0cc9c7b16" id="CMPD_0000000002" name="CMPD_0000000002" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
45 <annotation>
46 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
47 <rdf:Description rdf:about="#_7d22781170c09f66099e3d92f82fe456ce2c3f02d9162656e7ca49a0cc9c7b16">
48 <bqbiol:is>
49 <rdf:Bag/>
50 </bqbiol:is>
51 </rdf:Description>
52 <rdf:BRSynth rdf:about="#_7d22781170c09f66099e3d92f82fe456ce2c3f02d9162656e7ca49a0cc9c7b16">
53 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
54 <brsynth:smiles value="[H]OC(=O)C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H]"/>
55 <brsynth:inchi value="InChI=1S/C9H8O2/c10-9(11)7-6-8-4-2-1-3-5-8/h1-7H,(H,10,11)"/>
56 <brsynth:inchikey value="WBYWAXJHAXSJNI-UHFFFAOYSA-N"/>
57 </brsynth:brsynth>
58 </rdf:BRSynth>
59 </rdf:RDF>
60 </annotation>
61 </species>
62 <species metaid="_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251" id="MNXM13" name="MNXM13" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
63 <annotation>
64 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
65 <rdf:Description rdf:about="#_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251">
66 <bqbiol:is>
67 <rdf:Bag/>
68 </bqbiol:is>
69 </rdf:Description>
70 <rdf:BRSynth rdf:about="#_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251">
71 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
72 <brsynth:smiles value="O=C=O"/>
73 <brsynth:inchi value="InChI=1S/CO2/c2-1-3"/>
74 <brsynth:inchikey value="CURLTUGMZLYLDI-UHFFFAOYSA-N"/>
75 </brsynth:brsynth>
76 </rdf:BRSynth>
77 </rdf:RDF>
78 </annotation>
79 </species>
80 <species metaid="ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25" id="MNXM1" name="MNXM1" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
81 <annotation>
82 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
83 <rdf:Description rdf:about="#ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25">
84 <bqbiol:is>
85 <rdf:Bag/>
86 </bqbiol:is>
87 </rdf:Description>
88 <rdf:BRSynth rdf:about="#ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25">
89 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
90 <brsynth:smiles value="[H+]"/>
91 <brsynth:inchi value="InChI=1S/p+1"/>
92 <brsynth:inchikey value="GPRLSGONYQIRFK-UHFFFAOYSA-N"/>
93 </brsynth:brsynth>
94 </rdf:BRSynth>
95 </rdf:RDF>
96 </annotation>
97 </species>
98 <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
99 <annotation>
100 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
101 <rdf:Description rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
102 <bqbiol:is>
103 <rdf:Bag/>
104 </bqbiol:is>
105 </rdf:Description>
106 <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
107 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
108 <brsynth:smiles value="[H]C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H]"/>
109 <brsynth:inchi value="InChI=1S/C8H8/c1-2-8-6-4-3-5-7-8/h2-7H,1H2"/>
110 <brsynth:inchikey value="PPBRXRYQALVLMV-UHFFFAOYSA-N"/>
111 </brsynth:brsynth>
112 </rdf:BRSynth>
113 </rdf:RDF>
114 </annotation>
115 </species>
116 <species metaid="_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b" id="MNXM15" name="MNXM15" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
117 <annotation>
118 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
119 <rdf:Description rdf:about="#_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b">
120 <bqbiol:is>
121 <rdf:Bag/>
122 </bqbiol:is>
123 </rdf:Description>
124 <rdf:BRSynth rdf:about="#_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b">
125 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
126 <brsynth:smiles value="N"/>
127 <brsynth:inchi value="InChI=1S/H3N/h1H3"/>
128 <brsynth:inchikey value="QGZKDVFQNNGYKY-UHFFFAOYSA-N"/>
129 </brsynth:brsynth>
130 </rdf:BRSynth>
131 </rdf:RDF>
132 </annotation>
133 </species>
134 </listOfSpecies>
135 <listOfParameters>
136 <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_10000_0" value="10000" constant="true"/>
137 <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_0_0" value="0" constant="true"/>
138 </listOfParameters>
139 <listOfReactions>
140 <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0_0" fbc:upperFluxBound="BRS_FBC_10000_0">
141 <annotation>
142 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
143 <rdf:Description rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
144 <bqbiol:is>
145 <rdf:Bag>
146 <rdf:li rdf:resource="http://identifiers.org/ec-code/4.3.1.24"/>
147 <rdf:li rdf:resource="http://identifiers.org/ec-code/4.3.1.25"/>
148 </rdf:Bag>
149 </bqbiol:is>
150 </rdf:Description>
151 <rdf:BRSynth rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
152 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
153 <brsynth:smiles value="[H]OC(=O)C([H])(N([H])[H])C([H])([H])c1c([H])c([H])c([H])c([H])c1[H]&gt;&gt;[H]OC(=O)C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H].N"/>
154 <brsynth:rp2_transfo_id value="TRS_0_1_1"/>
155 <brsynth:rule_ids/>
156 <brsynth:tmpl_rxn_ids>
157 <brsynth:MNXR106649/>
158 <brsynth:MNXR131345/>
159 </brsynth:tmpl_rxn_ids>
160 <brsynth:rule_score value="0.5869134225065102"/>
161 <brsynth:idx_in_path value="1"/>
162 <brsynth:fba_biomass>
163 <brsynth:value value="0.0"/>
164 <brsynth:units value="gDW / gDW / hour"/>
165 </brsynth:fba_biomass>
166 <brsynth:fba_fraction>
167 <brsynth:value value="1.3666677776240859"/>
168 <brsynth:units value="milimole / gDW / hour"/>
169 </brsynth:fba_fraction>
170 <brsynth:thermo_dG0_prime>
171 <brsynth:value value="-3.619165315209898"/>
172 <brsynth:error value="0.5540714922475698"/>
173 <brsynth:units value="kilojoule / mole"/>
174 </brsynth:thermo_dG0_prime>
175 <brsynth:thermo_dGm_prime>
176 <brsynth:value value="-20.73400284993093"/>
177 <brsynth:error value="0.5540714922475698"/>
178 <brsynth:units value="kilojoule / mole"/>
179 </brsynth:thermo_dGm_prime>
180 <brsynth:thermo_dG_prime>
181 <brsynth:value value="-3.619165315209898"/>
182 <brsynth:error value="0.5540714922475698"/>
183 <brsynth:units value="kilojoule / mole"/>
184 </brsynth:thermo_dG_prime>
185 <brsynth:thermo_dG>
186 <brsynth:value value="-2.0435274124526472"/>
187 <brsynth:error value="0.5540714922475698"/>
188 <brsynth:units value="kilojoule / mole"/>
189 </brsynth:thermo_dG>
190 </brsynth:brsynth>
191 </rdf:BRSynth>
192 </rdf:RDF>
193 </annotation>
194 <listOfReactants>
195 <speciesReference species="MNXM97" stoichiometry="1" constant="true"/>
196 </listOfReactants>
197 <listOfProducts>
198 <speciesReference species="CMPD_0000000002" stoichiometry="1" constant="true"/>
199 <speciesReference species="MNXM15" stoichiometry="1" constant="true"/>
200 </listOfProducts>
201 </reaction>
202 <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0_0" fbc:upperFluxBound="BRS_FBC_10000_0">
203 <annotation>
204 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
205 <rdf:Description rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">
206 <bqbiol:is>
207 <rdf:Bag>
208 <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.1.102"/>
209 </rdf:Bag>
210 </bqbiol:is>
211 </rdf:Description>
212 <rdf:BRSynth rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">
213 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
214 <brsynth:smiles value="[H]OC(=O)C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H].[H+]&gt;&gt;O=C=O.[H]C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H]"/>
215 <brsynth:rp2_transfo_id value="TRS_0_0_0"/>
216 <brsynth:rule_ids/>
217 <brsynth:tmpl_rxn_ids>
218 <brsynth:MNXR114372/>
219 </brsynth:tmpl_rxn_ids>
220 <brsynth:rule_score value="1.0"/>
221 <brsynth:idx_in_path value="2"/>
222 <brsynth:fba_biomass>
223 <brsynth:value value="0.0"/>
224 <brsynth:units value="gDW / gDW / hour"/>
225 </brsynth:fba_biomass>
226 <brsynth:fba_fraction>
227 <brsynth:value value="1.3666677776240859"/>
228 <brsynth:units value="milimole / gDW / hour"/>
229 </brsynth:fba_fraction>
230 <brsynth:thermo_dG0_prime>
231 <brsynth:value value="-5.570411694686811"/>
232 <brsynth:error value="5.365139708628456"/>
233 <brsynth:units value="kilojoule / mole"/>
234 </brsynth:thermo_dG0_prime>
235 <brsynth:thermo_dGm_prime>
236 <brsynth:value value="-22.685249229407844"/>
237 <brsynth:error value="5.365139708628456"/>
238 <brsynth:units value="kilojoule / mole"/>
239 </brsynth:thermo_dGm_prime>
240 <brsynth:thermo_dG_prime>
241 <brsynth:value value="-5.570411694686811"/>
242 <brsynth:error value="5.365139708628456"/>
243 <brsynth:units value="kilojoule / mole"/>
244 </brsynth:thermo_dG_prime>
245 <brsynth:thermo_dG>
246 <brsynth:value value="-49.87811933289868"/>
247 <brsynth:error value="5.365139708628456"/>
248 <brsynth:units value="kilojoule / mole"/>
249 </brsynth:thermo_dG>
250 </brsynth:brsynth>
251 </rdf:BRSynth>
252 </rdf:RDF>
253 </annotation>
254 <listOfReactants>
255 <speciesReference species="CMPD_0000000002" stoichiometry="1" constant="true"/>
256 <speciesReference species="MNXM1" stoichiometry="1" constant="true"/>
257 </listOfReactants>
258 <listOfProducts>
259 <speciesReference species="MNXM13" stoichiometry="1" constant="true"/>
260 <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>
261 </listOfProducts>
262 </reaction>
263 </listOfReactions>
264 <groups:listOfGroups>
265 <groups:group metaid="_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299" groups:id="rp_pathway" groups:kind="collection">
266 <annotation>
267 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
268 <rdf:BRSynth rdf:about="#_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299">
269 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
270 <brsynth:fba_biomass>
271 <brsynth:value value="0.8769972144269752"/>
272 <brsynth:units value="gDW / gDW / hour"/>
273 </brsynth:fba_biomass>
274 <brsynth:fba_fraction>
275 <brsynth:value value="1.3666677776240859"/>
276 <brsynth:units value="milimole / gDW / hour"/>
277 </brsynth:fba_fraction>
278 <brsynth:thermo_dG0_prime>
279 <brsynth:value value="-9.189577009896766"/>
280 <brsynth:error value="5.336452836371218"/>
281 <brsynth:units value="kilojoule / mole"/>
282 </brsynth:thermo_dG0_prime>
283 <brsynth:thermo_dGm_prime>
284 <brsynth:value value="-43.41925207933883"/>
285 <brsynth:error value="5.336452836371218"/>
286 <brsynth:units value="kilojoule / mole"/>
287 </brsynth:thermo_dGm_prime>
288 <brsynth:thermo_dG_prime>
289 <brsynth:value value="-9.189577009896766"/>
290 <brsynth:error value="5.336452836371218"/>
291 <brsynth:units value="kilojoule / mole"/>
292 </brsynth:thermo_dG_prime>
293 <brsynth:thermo_dG>
294 <brsynth:value value="-51.92164674535138"/>
295 <brsynth:error value="5.336452836371218"/>
296 <brsynth:units value="kilojoule / mole"/>
297 </brsynth:thermo_dG>
298 <brsynth:global_score value="0.9923127055168152"/>
299 </brsynth:brsynth>
300 </rdf:BRSynth>
301 </rdf:RDF>
302 </annotation>
303 <groups:listOfMembers>
304 <groups:member groups:idRef="rxn_1"/>
305 <groups:member groups:idRef="rxn_2"/>
306 </groups:listOfMembers>
307 </groups:group>
308 <groups:group metaid="_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a" groups:id="rp_intermediate_species" groups:kind="collection">
309 <annotation>
310 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
311 <rdf:BRSynth rdf:about="#_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a">
312 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
313 </rdf:BRSynth>
314 </rdf:RDF>
315 </annotation>
316 <groups:listOfMembers>
317 <groups:member groups:idRef="CMPD_0000000002"/>
318 </groups:listOfMembers>
319 </groups:group>
320 <groups:group metaid="_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579" groups:id="rp_trunk_species" groups:kind="collection">
321 <annotation>
322 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
323 <rdf:BRSynth rdf:about="#_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579">
324 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
325 </rdf:BRSynth>
326 </rdf:RDF>
327 </annotation>
328 <groups:listOfMembers>
329 <groups:member groups:idRef="TARGET_0000000001"/>
330 <groups:member groups:idRef="MNXM97"/>
331 <groups:member groups:idRef="CMPD_0000000002"/>
332 </groups:listOfMembers>
333 </groups:group>
334 <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">
335 <annotation>
336 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
337 <rdf:BRSynth rdf:about="#_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378">
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360 <groups:member groups:idRef="MNXM97"/>
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372 <groups:group metaid="fb9b29ba20af773fed953f1d6726905a453f235c9a4baa7217f02760bc2057f8" groups:id="rp_thermo_substituted_species" groups:kind="collection">
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380 </groups:group>
381 </groups:listOfGroups>
382 </model>
383 </sbml>